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- EMDB-54214: Rab23 in complex with Fuzzy-Inturned -

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Basic information

Entry
Database: EMDB / ID: EMD-54214
TitleRab23 in complex with Fuzzy-Inturned
Map data
Sample
  • Complex: human Rab23 with GEF Fuzzy-Inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Protein inturned
    • Protein or peptide: Ras-related protein Rab-23
Keywordslongin domain / GEF / nucleotide exchange / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / craniofacial suture morphogenesis / embryonic body morphogenesis / spinal cord dorsal/ventral patterning / establishment of planar polarity / protein localization to organelle / intraciliary transport / regulation of cilium assembly ...negative regulation of neural crest formation / negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation / tongue morphogenesis / craniofacial suture morphogenesis / embryonic body morphogenesis / spinal cord dorsal/ventral patterning / establishment of planar polarity / protein localization to organelle / intraciliary transport / regulation of cilium assembly / ciliary transition zone / embryonic skeletal system morphogenesis / motile cilium assembly / negative regulation of cell division / positive regulation of cilium assembly / RAB geranylgeranylation / non-motile cilium assembly / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / GTP metabolic process / limb development / neural tube development / motile cilium / embryonic digit morphogenesis / hair follicle morphogenesis / smoothened signaling pathway / negative regulation of protein import into nucleus / roof of mouth development / regulation of ossification / cilium assembly / autophagosome assembly / hair follicle development / negative regulation of keratinocyte proliferation / cellular defense response / Hedgehog 'off' state / keratinocyte differentiation / phagocytic vesicle / vesicle-mediated transport / centriole / endomembrane system / phosphatidylinositol binding / autophagosome / negative regulation of cell migration / small monomeric GTPase / neural tube closure / intracellular protein transport / negative regulation of canonical Wnt signaling pathway / phagocytic vesicle membrane / cell junction / nervous system development / protein transport / cytoskeleton / endosome membrane / cilium / ciliary basal body / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / GTP binding / cell surface / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fuzzy protein / Protein inturned / Ras-related protein Rab-23 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain ...Fuzzy protein / Protein inturned / Ras-related protein Rab-23 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / PDZ superfamily / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein fuzzy homolog / Ras-related protein Rab-23 / Protein inturned
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWilmes S / Schaefer J / Januliene D / Moeller A / Kuemmel D
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557-P10 Germany
German Research Foundation (DFG)SFB1557-P11 Germany
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.
Authors: Stephan Wilmes / Jesse Tönjes / Maik Drechsler / Anita Ruf / Jan-Hannes Schäfer / Anna Lürick / Dovile Januliene / Steven Apelt / Daniele Di Iorio / Seraphine V Wegner / Martin Loose / ...Authors: Stephan Wilmes / Jesse Tönjes / Maik Drechsler / Anita Ruf / Jan-Hannes Schäfer / Anna Lürick / Dovile Januliene / Steven Apelt / Daniele Di Iorio / Seraphine V Wegner / Martin Loose / Arne Moeller / Achim Paululat / Daniel Kümmel /
Abstract: Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure ...Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure fidelity. Our structural and functional comparison of the tri-longin domain RabGEFs Mon1-Ccz1 and Fuzzy-Inturned reveals the molecular basis for their target specificity. Both complexes rely on a conserved sequence motif of their substrate GTPases for the catalytic mechanism, while secondary interactions allow discrimination between targets. We also find that dimeric Mon1-Ccz1 from fungi and the metazoan homologs with the additional third subunit RMC1/Bulli bind membranes through electrostatic interactions via distinct interfaces. Protein-lipid interaction studies and functional characterization in flies reveal an essential function of RMC1/Bulli as mediator of GEF complex membrane recruitment. In the case of Fuzzy-Inturned, reconstitution experiments demonstrate that the BAR (Bin-Amphiphysin-Rvs) domain protein CiBAR1 can support membrane recruitment of the GEF. Collectively, our study demonstrates the molecular basis for the adaptation of TLD-RabGEFs to different cellular functions.
History
DepositionJun 30, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54214.png

Downloads & links

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Map

FileDownload / File: emd_54214.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0329
Minimum - Maximum-0.14107043 - 0.24603589
Average (Standard dev.)0.00019014096 (±0.0061901486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54214_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54214_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : human Rab23 with GEF Fuzzy-Inturned

EntireName: human Rab23 with GEF Fuzzy-Inturned
Components
  • Complex: human Rab23 with GEF Fuzzy-Inturned
    • Protein or peptide: Protein fuzzy homolog
    • Protein or peptide: Protein inturned
    • Protein or peptide: Ras-related protein Rab-23

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Supramolecule #1: human Rab23 with GEF Fuzzy-Inturned

SupramoleculeName: human Rab23 with GEF Fuzzy-Inturned / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein fuzzy homolog

MacromoleculeName: Protein fuzzy homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.689883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: VGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS ...String:
VGEEGTGGTV HLLCLAASSG VPLFCRSSRG GAPARQQLPF SVIGSLNGVH MFGQNLEVQL SSARTENTTV VWKSFHDSIT LIVLSSEVG ISELRLERLL QMVFGAMVLL VGLEELTNIR NVERLKKDLR ASYCLIDSFL GDSELIGDLT QCVDCVIPPE G SLLQEALS GFAEAAGTTF VSLVVSGRVV AATEGWWRLG TPEAVLLPWL VGSLPPQTAR DYPVYLPHGS PTVPHRLLTL TL LPSLELC LLCGPSPPLS QLYPQLLERW WQPLLDPLRA CLPLGPRALP SGFPLHTDIL GLLLLHLELK RCLFTVEPLG DKE PSPEQR RRLLRNFYTL VTSTHFPPEP GPPEKTEDEV YQAQLPRACY LVLGTEEPGT GVRLVALQLG LRRLLLLLSP QSPT HGLRS LATHTLHALT PLL

UniProtKB: Protein fuzzy homolog

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Macromolecule #2: Protein inturned

MacromoleculeName: Protein inturned / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.526023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG VPRIPMASVA SCDSRPSSDE LPGDPSSQEE DEDYDFEDRV SDSGSYSSAS SDYDDLEPEW LDSVQKNGEL FYLELSEDE EESLLPETPT VNHVRFSENE IIIEDDYKER KKYEPKLKQF TKILRRKRLL PKRCNKKNSN DNGPVSILKH Q SNQKTGVI ...String:
MDYKDDDDKG VPRIPMASVA SCDSRPSSDE LPGDPSSQEE DEDYDFEDRV SDSGSYSSAS SDYDDLEPEW LDSVQKNGEL FYLELSEDE EESLLPETPT VNHVRFSENE IIIEDDYKER KKYEPKLKQF TKILRRKRLL PKRCNKKNSN DNGPVSILKH Q SNQKTGVI VQQRYKDVNV YVNPKKLTVI KAKEQLKLLE VLVGIIHQTK WSWRRTGKQG DGERLVVHGL LPGGSAMKSG QV LIGDVLV AVNDVDVTTE NIERVLSCIP GPMQVKLTFE NAYDVKRETS HPRQKKTQSN TSDLVKLLWG EEVEGIQQSG LNT PHIIMY LTLQLDSETS KEEQEILYHY PMSEASQKLK SVRGIFLTLC DMLENVTGTQ VTSSSLLLNG KQIHVAYWKE SDKL LLIGL PAEEVPLPRL RNMIENVIQT LKFMYGSLDS AFCQIENVPR LDHFFNLFFQ RALQPAKLHS SASPSAQQYD ASSAV LLDN LPGVRWLTLP LEIKMELDMA LSDLEAADFA ELSEDYYDMR RLYTILGSSL FYKGYLICSH LPKDDLIDIA VYCRHY CLL PLAAKQRIGQ LIIWREVFPQ HHLRPLADSS TEVFPEPEGR YFLLVVGLKH YMLCVLLEAG GCASKAIGSP GPDCVYV DQ VKTTLHQLDG VDSRIDERLA SSPVPCLSCA DWFLTGSREK TDSLTTSPIL SRLQGTSKVA TSPTCRRTLF GDYSLKTR K PSPSCSSGGS DNGCEGGEDD GFSPHTTPDA VRKQRESQGS DGLEESGTLL KVTKKKSTLP NPFHLGNLKK DLPEKELEI YNTVKLTSGP ENTLFHYVAL ETVQGIFITP TLEEVAQLSG SIHPQLIKNF HQCCLSIRAV FQQTLVEEKK KGLNSGDHSD SAKSVSSLN PVKEHGVLFE CSPGNWTDQK KAPPVMAYWV VGRLFLHPKP QELYVCFHDS VTEIAIEIAF KLFFGLTL

UniProtKB: Protein inturned

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Macromolecule #3: Ras-related protein Rab-23

MacromoleculeName: Ras-related protein Rab-23 / type: protein_or_peptide / ID: 3 / Details: N121I / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.492129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPLGSEFELL EEDMEVAIKM VVVGNGAVGK SSMIQRYCKG IFTKDYKKTI GVDFLERQIQ VNDEDVRLML WDTAGQEEFD AITKAYYRG AQACVLVFST TDRESFEAVS SWREKVVAEV GDIPTVLVQI KIDLLDDSCI KNEEAEALAK RLKLRFYRTS V KEDLNVNE ...String:
GPLGSEFELL EEDMEVAIKM VVVGNGAVGK SSMIQRYCKG IFTKDYKKTI GVDFLERQIQ VNDEDVRLML WDTAGQEEFD AITKAYYRG AQACVLVFST TDRESFEAVS SWREKVVAEV GDIPTVLVQI KIDLLDDSCI KNEEAEALAK RLKLRFYRTS V KEDLNVNE VFKYLAEKYL QKLKQQIAED PELTHSSSNK IGVFNTSGGS HSGQNSGTLN GGDVINLRPN KQRTKKNRNP FS SCSIP

UniProtKB: Ras-related protein Rab-23

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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